Genetic constraints on adaptation to a changing environment

The potential for evolutionary rescue in an Arctic seashore plant threatened by climate change

The impacts of climate change may be particularly severe for geographically isolated populations, which must adjust through plastic responses or evolve. Here, we study an endangered Arctic plant, Primula nutans ssp. finmarchica, confined to Fennoscandian seashores and showing indications of maladaptation to warming climate. We evaluate the potential of these populations to evolve to facilitate survival in the rapidly warming Arctic (i.e. evolutionary rescue) by utilizing manual crossing experiments in a nested half-sibling breeding design. We estimate G-matrices, evolvability and genetic constraints in traits with potentially conflicting selection pressures. To explicitly evaluate the potential for climate change adaptation, we infer the expected time to evolve from a northern to a southern phenotype under different selection scenarios, using demographic and climatic data to relate expected evolutionary rates to projected rates of climate change. Our results indicate that, given the nearly 10-fold greater evolvability of vegetative than of floral traits, adaptation in these traits may take place nearly in concert with changing climate, given effective climate mitigation. However, the comparatively slow expected evolutionary modification of floral traits may hamper the evolution of floral traits to track climate-induced changes in pollination environment, compromising sexual reproduction and thus reducing the likelihood of evolutionary rescue.

Effect of the Seed Bank on Evolutionary Rescue in Small Populations: Univariate and Multivariate Demogenetic Dynamics

AbstractUnder global change, the impact of seed banks on evolutionary rescue is uncertain. They buffer plant populations from demographic and genetic stochasticity but extend generation time and can become a reservoir of maladapted alleles. We built analytical and individual-based models to predict the effect of seed banks on the persistence of small annual plant populations facing an abrupt or sustained directional change in uni- or multivariate trait optima. Demogenetic dynamics predict that under most scenarios seed banks increase the lag yet enhance persistence to 200-250 years by absorbing demographic losses. Simulations indicate that the seed bank has a minimal impact on the genetic skew, although we suggest that this result could depend on the fitness component under selection. Our multivariate model reveals that by enlarging and reshaping the G matrix, seed banks can diminish the impact of mutational correlation and even accelerate adaptation under antagonistic pleiotropy relative to populations without a bank. We illustrate how the magnitude of optimum fluctuations, type and degree of optimum change, selection strength, and vital rates are weights that tip the scales determining persistence. Finally, our work highlights that migration from the past is not maladaptative when optimum fluctuations are large enough to create stepping stones to the new optimum.

Dolphin social phenotypes vary in response to food availability but not the North Atlantic Oscillation index

Social behaviours can allow individuals to flexibly respond to environmental change, potentially buffering adverse effects. However, individuals may respond differently to the same environmental stimulus, complicating predictions for population-level response to environmental change. Here, we show that bottlenose dolphins (Tursiops truncatus) alter their social behaviour at yearly and monthly scales in response to a proxy for food availability (salmon abundance) but do not respond to variation in a proxy for climate (the North Atlantic Oscillation index). There was also individual variation in plasticity for gregariousness and connectedness to distant parts of the social network, although these traits showed limited repeatability. By contrast, individuals showed consistent differences in clustering with their immediate social environment at the yearly scale but no individual variation in plasticity for this trait at either timescale. These results indicate that social behaviour in free-ranging cetaceans can be highly resource dependent with individuals increasing their connectedness over short timescales but possibly reducing their wider range of connection at longer timescales. Some social traits showed more individual variation in plasticity or mean behaviour than others, highlighting how predictions for the responses of populations to environmental variation must consider the type of individual variation present in the population.

Exact expressions and numerical evaluation of average evolvability measures for characterizing and comparing [Formula: see text] matrices

Theory predicts that the additive genetic covariance ([Formula: see text]) matrix determines a population's short-term (in)ability to respond to directional selection-evolvability in the Hansen-Houle sense-which is typically quantified and compared via certain scalar indices called evolvability measures. Often, interest is in obtaining the averages of these measures across all possible selection gradients, but explicit formulae for most of these average measures have not been known. Previous authors relied either on approximations by the delta method, whose accuracy is generally unknown, or Monte Carlo evaluations (including the random skewers analysis), which necessarily involve random fluctuations. This study presents new, exact expressions for the average conditional evolvability, average autonomy, average respondability, average flexibility, average response difference, and average response correlation, utilizing their mathematical structures as ratios of quadratic forms. The new expressions are infinite series involving top-order zonal and invariant polynomials of matrix arguments, and can be numerically evaluated as their partial sums with, for some measures, known error bounds. Whenever these partial sums numerically converge within reasonable computational time and memory, they will replace the previous approximate methods. In addition, new expressions are derived for the average measures under a general normal distribution for the selection gradient, extending the applicability of these measures into a substantially broader class of selection regimes.

Can extreme climatic events induce shifts in adaptive potential? A conceptual framework and empirical test with Anolis lizards

Multivariate adaptation to climatic shifts may be limited by trait integration that causes genetic variation to be low in the direction of selection. However, strong episodes of selection induced by extreme climatic pressures may facilitate future population-wide responses if selection reduces trait integration and increases adaptive potential (i.e., evolvability). We explain this counter-intuitive framework for extreme climatic events in which directional selection leads to increased evolvability and exemplify its use in a case study. We tested this hypothesis in two populations of the lizard Anolis scriptus that experienced hurricane-induced selection on limb traits. We surveyed populations immediately before and after the hurricane as well as the offspring of post-hurricane survivors, allowing us to estimate both selection and response to selection on key functional traits: forelimb length, hindlimb length, and toepad area. The direct selection was parallel in both islands and strong in several limb traits. Even though overall limb integration did not change after the hurricane, both populations showed a non-significant tendency toward increased evolvability after the hurricane despite the direction of selection not being aligned with the axis of most variance (i.e., body size). The population with comparably lower between-limb integration showed a less constrained response to selection. Hurricane-induced selection, not aligned with the pattern of high trait correlations, likely conflicts with selection occurring during normal ecological conditions that favours functional coordination between limb traits, and would likely need to be very strong and more persistent to elicit a greater change in trait integration and evolvability. Future tests of this hypothesis should use G-matrices in a variety of wild organisms experiencing selection due to extreme climatic events.

Precipitation predictability affects intra- and trans-generational plasticity and causes differential selection on root traits of Papaver rhoeas

Climate forecasts show that in many regions the temporal distribution of precipitation events will become less predictable. Root traits may play key roles in dealing with changes in precipitation predictability, but their functional plastic responses, including transgenerational processes, are scarcely known. We investigated root trait plasticity of Papaver rhoeas with respect to higher versus lower intra-seasonal and inter-seasonal precipitation predictability (i.e., the degree of temporal autocorrelation among precipitation events) during a four-year outdoor multi-generation experiment. We first tested how the simulated predictability regimes affected intra-generational plasticity of root traits and allocation strategies of the ancestors, and investigated the selective forces acting on them. Second, we exposed three descendant generations to the same predictability regime experienced by their mothers or to a different one. We then investigated whether high inter-generational predictability causes root trait differentiation, whether transgenerational root plasticity existed and whether it was affected by the different predictability treatments. We found that the number of secondary roots, root biomass and root allocation strategies of ancestors were affected by changes in precipitation predictability, in line with intra-generational plasticity. Lower predictability induced a root response, possibly reflecting a fast-acquisitive strategy that increases water absorbance from shallow soil layers. Ancestors' root traits were generally under selection, and the predictability treatments did neither affect the strength nor the direction of selection. Transgenerational effects were detected in root biomass and root weight ratio (RWR). In presence of lower predictability, descendants significantly reduced RWR compared to ancestors, leading to an increase in performance. This points to a change in root allocation in order to maintain or increase the descendants' fitness. Moreover, transgenerational plasticity existed in maximum rooting depth and root biomass, and the less predictable treatment promoted the lowest coefficient of variation among descendants' treatments in five out of six root traits. This shows that the level of maternal predictability determines the variation in the descendants' responses, and suggests that lower phenotypic plasticity evolves in less predictable environments. Overall, our findings show that roots are functional plastic traits that rapidly respond to differences in precipitation predictability, and that the plasticity and adaptation of root traits may crucially determine how climate change will affect plants.

The importance of considering the duration of extreme temperatures when investigating responses to climate change

The frequency and duration of heatwaves are increasing because of human activities. To cope with the changes, species with longer generation times may have to rely on plastic responses. The probability that their responses are adaptive is higher if the species have experienced temperature fluctuations also in their evolutionary past. However, experimental studies investigating responses to heatwaves often use exposure times that are significantly shorter than recent heatwaves. We show that this can lead to faulty conclusions and that the duration of higher temperature has to be considered in experimental designs. We recorded the response of threespine stickleback to prolonged duration of higher temperature during the breeding season, using a population that has experienced large fluctuations in temperature in its past and, hence, is expected to endure temperature changes well. We found males to adaptively adjust their reproductive behaviours to short periods of higher temperature, but not to longer periods that extended across two breeding cycles. Males initially increased their reproductive activities-nest building, courtship and parental care-which ensured high reproductive success during the first breeding cycle, but decreased their reproductive activities during the second breeding cycle when exposed to sustained high temperature. This reduced their courtship success and resulted in fewer offspring. Thus, a species expected to cope well with higher temperature suffers fitness reductions when the duration of high temperature is prolonged. The results stress the importance of considering the duration of extreme environmental conditions when investigating the impact that human activities have on species. Responses to short-term exposures cannot be extrapolated to assess responses to longer periods of extreme conditions.

Increasing temporal variance leads to stable species range limits

What prevents populations of a species from adapting to the novel environments outside the species' geographic distribution? Previous models highlighted how gene flow across spatial environmental gradients determines species expansion versus extinction and the location of species range limits. However, space is only one of two axes of environmental variation-environments also vary in time, and we know temporal environmental variation has important consequences for population demography and evolution. We used analytical and individual-based evolutionary models to explore how temporal variation in environmental conditions influences the spread of populations across a spatial environmental gradient. We find that temporal variation greatly alters our predictions for range dynamics compared to temporally static environments. When temporal variance is equal across the landscape, the fate of species (expansion versus extinction) is determined by the interaction between the degree of temporal autocorrelation in environmental fluctuations and the steepness of the spatial environmental gradient. When the magnitude of temporal variance changes across the landscape, stable range limits form where this variance increases maladaptation sufficiently to prevent local persistence. These results illustrate the pivotal influence of temporal variation on the likelihood of populations colonizing novel habitats and the location of species range limits.

Sexual dimorphism in phenotypic plasticity and persistence under environmental change: An extension of theory and meta-analysis of current data

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity-particularly in traits with modest-to-low cross-sex genetic correlations-typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception-cold resistance-is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

Evolvability: A Quantitative-Genetics Perspective

The concept of evolvability emerged in the early 1990s and soon became fashionable as a label for different streams of research in evolutionary biology. In evolutionary quantitative genetics, evolvability is defined as the ability of a population to respond to directional selection. This differs from other fields by treating evolvability as a property of populations rather than organisms or lineages and in being focused on quantification and short-term prediction rather than on macroevolution. While the term evolvability is new to quantitative genetics, many of the associated ideas and research questions have been with the field from its inception as biometry. Recent research on evolvability is more than a relabeling of old questions, however. New operational measures of evolvability have opened possibilities for understanding adaptation to rapid environmental change, assessing genetic constraints, and linking micro- and macroevolution.

Allen Orr and the genetics of adaptation

Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.

Is Evolution in Response to Extreme Events Good for Population Persistence?

AbstractClimate change is predicted to increase the severity of environmental perturbations, including storms and droughts, which act as strong selective agents. These extreme events are often of finite duration (pulse disturbances). Hence, while evolution during an extreme event may be adaptive, the resulting phenotypic changes may become maladaptive when the event ends. Using individual-based models and analytic approximations that fuse quantitative genetics and demography, we explore how heritability and phenotypic variance affect population size and extinction risk in finite populations under an extreme event of fixed duration. Since more evolution leads to greater maladaptation and slower population recovery following an extreme event, greater heritability can increase extinction risk when the extreme event is short. Alternatively, when an extreme event is sufficiently long, heritability often helps a population persist. We also find that when events are severe, the buffering effect of phenotypic variance can outweigh the increased load it causes.

Ecological causes of fluctuating natural selection on habitat choice in an amphibian

We estimated natural selection targeting three traits related to habitat choice in a frog (Pseudacris maculata) breeding in pools on the rocky shores of Isle Royale, Michigan, over 16 years. Our aim was to identify the form and ecological causes of annual variation in directional and correlational selection as expressed in the survival and growth of tadpoles. We found directional selection favoring early breeding, but pool choice was under weak stabilizing selection. However, the form of stabilizing selection and the position of the optimum trait value shifted among years with the severity of disturbance and the intensity of biotic interactions. In years when wave wash and pool desiccation were severe, selection shifted to favor tadpoles in habitats where these risks were less pronounced. If predatory dragonfly larvae were abundant, selection favored tadpoles in small pools where dragonflies did not occur. When intraspecific competition was strong, selection favored early broods within a broader range of pool types. The agents of selection in this study—biotic interactions and disturbance—are common to many ecological systems and frequently exhibit temporal variation; this suggests that fluctuating selection may be widespread in natural populations.

Does Phenological Plasticity Help or Hinder Range Shifts Under Climate Change?

Climate warming is predicted to shift species’ ranges as previously uninhabitable environments just beyond the leading range edges become suitable habitat and trailing range edges become increasingly unsuitable. Understanding which aspects of the environment and species traits mediate these range shifts is critical for understanding species’ possible redistributions under global change, yet we have a limited understanding of the ecological and evolutionary responses underlying population spread or extinction at species’ range edges. Within plant populations, shifts in flowering phenology have been one of the strongest and most consistent responses to climate change, and are likely to play an important role in mediating population dynamics within and beyond species’ ranges. However, the role of phenological shifts, and particularly phenological plasticity, in species’ range shifts remains relatively unstudied. Here, we synthesize literature on phenology, plasticity, and adaptation to suggest ways in which phenological responses to climate may vary across species’ ranges and review the empirical evidence for and against these hypotheses. We then outline how phenological plasticity could facilitate or hinder persistence and potential consequences of phenological plasticity in range expansions, including phenological cues, shifts in correlated traits, altered species interactions, and effects on gene flow. Finally, we suggest future avenues for research, such as characterizing reaction norms for phenology across a species’ range and in beyond-the-range transplant experiments. Given the prevalence and magnitude of phenological shifts, future work should carefully dissect its costs and benefits for population persistence, and incorporate phenological plasticity into models predicting species’ persistence and geographic range shifts under climate change.

The sources of variation for individual prey-to-predator size ratios

The relative body size at which predators are willing to attack prey, a key trait for predator-prey interactions, is usually considered invariant. However, this ratio can vary widely among individuals or populations. Identifying the range and origin of such variation is key to understanding the strength and constraints on selection in both predators and prey. Still, these sources of variation remain largely unknown. We filled this gap by measuring the genetic, maternal and environmental variation of the maximum prey-to-predator size ratio (PPSR_max) in juveniles of the wolf spider Lycosa fasciiventris using a paternal half-sib split-brood design, in which each male was paired with two females and the offspring reared in two food environments: poor and rich. Each juvenile spider was then sequentially offered crickets of decreasing size and the maximum prey size killed was determined. We also measured body size and body condition of spiders upon emergence and just before the trial. We found low, but significant heritability (h² = 0.069) and dominance and common environmental variance (d² + 4c² = 0.056). PPSR_max was also partially explained by body condition (during trial) but there was no effect of the rearing food environment. Finally, a maternal correlation between body size early in life and PPSR_max indicated that offspring born larger were less predisposed to feed on larger prey later in life. Therefore, PPSR_max, a central trait in ecosystems, can vary widely and this variation is due to different sources, with important consequences for changes in this trait in the short and long terms.

How does the strength of selection influence genetic correlations?

Genetic correlations between traits can strongly impact evolutionary responses to selection, and may thus impose constraints on adaptation. Theoretical and empirical work has made it clear that without strong linkage and with random mating, genetic correlations at evolutionary equilibrium result from an interplay of correlated pleiotropic effects of mutations, and correlational selection favoring combinations of trait values. However, it is not entirely clear how change in the overall strength of stabilizing selection across traits (breadth of the fitness peak, given its shape) influences this compromise between mutation and selection effects on genetic correlation. Here, we show that the answer to this question crucially depends on the intensity of genetic drift. In large, effectively infinite populations, genetic correlations are unaffected by the strength of selection, regardless of whether the genetic architecture involves common small-effect mutations (Gaussian regime), or rare large-effect mutations (House-of-Cards regime). In contrast in finite populations, the strength of selection does affect genetic correlations, by shifting the balance from drift-dominated to selection-dominated evolutionary dynamics. The transition between these domains depends on mutation parameters to some extent, but with a similar dependence of genetic correlation on the strength of selection. Our results are particularly relevant for understanding how senescence shapes patterns of genetic correlations across ages, and genetic constraints on adaptation during colonization of novel habitats.

Ecological limits to evolutionary rescue

Environments change, for both natural and anthropogenic reasons, which can threaten species persistence. Evolutionary adaptation is a potentially powerful mechanism to allow species to persist in these changing environments. To determine the conditions under which adaptation will prevent extinction (evolutionary rescue), classic quantitative genetics models have assumed a constantly changing environment. They predict that species traits will track a moving environmental optimum with a lag that approaches a constant. If fitness is negative at this lag, the species will go extinct. There have been many elaborations of these models incorporating increased genetic realism. Here, we review and explore the consequences of four ecological complications: non-quadratic fitness functions, interacting density- and trait-dependence, species interactions and fundamental limits to adaptation. We show that non-quadratic fitness functions can result in evolutionary tipping points and existential crises, as can the interaction between density- and trait-dependent mortality. We then review the literature on how interspecific interactions affect adaptation and persistence. Finally, we suggest an alternative theoretical framework that considers bounded environmental change and fundamental limits to adaptation. A research programme that combines theory and experiments and integrates across organizational scales will be needed to predict whether adaptation will prevent species extinction in changing environments. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics

Sexually antagonistic (SA) genetic variation-in which alleles favored in one sex are disfavored in the other-is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterization of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research-including F ST and F IS statistics, genome-wide association studies, pedigree analyses, reciprocal transplant studies, and evolve-and-resequence experiments-to evaluate methods for identifying SA genes and genome-wide signals of SA genetic variation. We begin by developing theoretical models for between-sex F ST and F IS, including explicit null distributions for each statistic, and using them to critically evaluate putative multilocus signals of sex-specific selection in previously published datasets. We then highlight new statistics that address some of the limitations of F ST and F IS, along with applications of more direct approaches for characterizing SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.

Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios

Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.

Natural and human-induced environmental changes and their effects on adaptive potential of wild animal populations

A major challenge of evolutionary ecology over the next decades is to understand and predict the consequences of the current rapid and important environmental changes on wild populations. Extinction risk of species is linked to populations' evolutionary potential and to their ability to express adaptive phenotypic plasticity. There is thus a vital need to quantify how selective pressures, quantitative genetics parameters, and phenotypic plasticity, for multiple traits in wild animal populations, may vary with changes in the environment. Here I review our previous research that integrated ecological and evolutionary theories with molecular ecology, quantitative genetics, and long-term monitoring of individually marked wild animals. Our results showed that assessing evolutionary and plastic changes over time and space, using multi-trait approaches, under a realistic range of environmental conditions are crucial steps toward improving our understanding of the evolution and adaptation of natural populations. Our current and future work focusses on assessing the limits of adaptive potential by determining the factors constraining the evolvability of plasticity, those generating covariation among genetic variance and selection, as well as indirect genetic effects, which can affect population's capacity to adjust to environmental changes. In doing so, we aim to provide an improved assessment of the spatial and temporal scale of evolutionary processes in wild animal populations.

Different genetic basis for alcohol dehydrogenase activity and plasticity in a novel alcohol environment for Drosophila melanogaster

Phenotypic plasticity is known to enhance population persistence, facilitate adaptive evolution and initiate novel phenotypes in novel environments. How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh-coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0 and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects, and that the Adh locus is not environmentally sensitive to dietary alcohol.

Fluctuations in lifetime selection in an autocorrelated environment

Most natural environments vary stochastically and are temporally autocorrelated. Previous theory investigating the effects of environmental autocorrelation on evolution mostly assumed that total fitness resulted from a single selection episode. Yet organisms are likely to experience selection repeatedly along their life, in response to possibly different environmental states. We model the evolution of a quantitative trait in organisms with non-overlapping generations undergoing several episodes of selection in a randomly fluctuating and autocorrelated environment. We show that the evolutionary dynamics depends not directly on fluctuations of the environment, but instead on those of an effective phenotypic optimum that integrates the effects of all selection episodes within each generation. The variance and autocorrelation of the integrated optimum shape the variance and predictability of selection, with substantial qualitative and quantitative deviations from previous predictions considering a single selection episode per generation. We also investigate the consequence of multiple selection episodes per generation on population load. In particular, we identify a new load resulting from within-generation fluctuating selection, generating the death of individuals without significance for the evolutionary dynamics. Our study emphasizes how taking into account fluctuating selection within lifetime unravels new properties of evolutionary dynamics, with crucial implications notably with respect to responses to global changes.

Experimental migration upward in elevation is associated with strong selection on life history traits

One of the strongest biological impacts of climate change has been the movement of species poleward and upward in elevation. Yet, what is not clear is the extent to which the spatial distribution of locally adapted lineages and ecologically important traits may also shift with continued climate change. Here, we take advantage of a transplant experiment mimicking up-slope seed dispersal for a suite of ecologically diverse populations of yellow monkeyflower (Mimulus guttatus sensu lato) into a high-elevation common garden during an extreme drought period in the Sierra Nevada mountains, California, USA. We use a demographic approach to quantify fitness and test for selection on life history traits in local versus lower-elevation populations and in normal versus drought years to test the potential for up-slope migration and phenotypic selection to alter the distribution of key life history traits in montane environments. We find that lower-elevation populations tend to outperform local populations, confirming the potential for up-slope migration. Although selection generally favored some local montane traits, including larger flowers and larger stem size at flowering, drought conditions tended to select for earlier flowering typical of lower-elevation genotypes. Taken together, this suggests that monkeyflower lineages moving upward in elevation could experience selection for novel trait combinations, particularly under warmer and drier conditions that are predicted to occur with continued climate change.

Selective Sweep at a QTL in a Randomly Fluctuating Environment

Adaptation is mediated by phenotypic traits that are often near continuous, and undergo selective pressures that may change with the environment. The dynamics of allelic frequencies at underlying quantitative trait loci (QTL) depend on their own phenotypic effects, but also possibly on other polymorphic loci affecting the same trait, and on environmental change driving phenotypic selection. Most environments include a substantial component of random noise, characterized both by its magnitude and its temporal autocorrelation, which sets the timescale of environmental predictability. I investigate the dynamics of a mutation affecting a quantitative trait in an autocorrelated stochastic environment that causes random fluctuations of an optimum phenotype. The trait under selection may also exhibit background polygenic variance caused by many polymorphic loci of small effects elsewhere in the genome. In addition, the mutation at the QTL may affect phenotypic plasticity, the phenotypic response of given genotype to its environment of development or expression. Stochastic environmental fluctuations increase the variance of the evolutionary process, with consequences for the probability of a complete sweep at the QTL. Background polygenic variation critically alters this process, by setting an upper limit to stochastic variance of population genetics at the QTL. For a plasticity QTL, stochastic fluctuations also influences the expected selection coefficient, and alleles with the same expected trajectory can have very different stochastic variances. Finally, a mutation may be favored through its effect on plasticity despite causing a systematic mismatch with optimum, which is compensated by evolution of the mean background phenotype.

Climate change shifts natural selection and the adaptive potential of the perennial forb Boechera stricta in the Rocky Mountains

Heritable genetic variation is necessary for populations to evolve in response to anthropogenic climate change. However, antagonistic genetic correlations among traits may constrain the rate of adaptation, even if substantial genetic variation exists. We examine potential genetic responses to selection by comparing multivariate genetic variance-covariances of traits and fitness (multivariate Robertson-Price identities) across different environments in a reciprocal transplant experiment of the forb Boechera stricta in the Rocky Mountains. By transplanting populations into four common gardens arrayed along an elevational gradient, and exposing populations to control and snow removal treatments, we simulated future and current climates and snowmelt regimes. Genetic variation in flowering and germination phenology declined in plants moved downslope to warmer, drier sites, suggesting that these traits may have a limited ability to evolve under future climates. Simulated climate change via snow removal altered the strength of selection on flowering traits, but we found little evidence that genetic correlations among traits are likely to affect the rate of adaptation to climate change. Overall, our results suggest that climate change may alter the evolutionary potential of B. stricta, but reduced expression of genetic variation may be a larger impediment to adaptation than constraints imposed by antagonistic genetic correlations.

Quantifying maladaptation during the evolution of sexual dimorphism

Females and males have distinct trait optima, resulting in selection for sexual dimorphism. However, most traits have strong cross-sex genetic correlations, which constrain evolutionary divergence between the sexes and lead to protracted periods of maladaptation during the evolution of sexual dimorphism. While such constraints are thought to be costly in terms of individual and population fitness, it remains unclear how severe such costs are likely to be. Building upon classical models for the 'cost of selection' in changing environments (sensu Haldane), we derived a theoretical expression for the analogous cost of evolving sexual dimorphism; this cost is a simple function of genetic (co)variances of female and male traits and sex differences in trait optima. We then conducted a comprehensive literature search, compiled quantitative genetic data from a diverse set of traits and populations, and used them to quantify costs of sexual dimorphism in the light of our model. For roughly 90% of traits, costs of sexual dimorphism appear to be modest, and comparable to the costs of fixing one or a few beneficial substitutions. For the remaining traits (approx. 10%), sexual dimorphism appears to carry a substantial cost-potentially orders of magnitude greater than costs of selection during adaptation to environmental changes.

Genomics of Developmental Plasticity in Animals

Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.

How frequency-dependent selection affects population fitness, maladaptation and evolutionary rescue

Frequency-dependent (FD) selection is a central process maintaining genetic variation and mediating evolution of population fitness. FD selection has attracted interest from researchers in a wide range of biological subdisciplines, including evolutionary genetics, behavioural ecology and, more recently, community ecology. However, the implications of frequency dependence for applied biological problems, particularly maladaptation, biological conservation and evolutionary rescue remain underexplored. The neglect of FD selection in conservation is particularly unfortunate. Classical theory, dating back to the 1940s, demonstrated that frequency dependence can either increase or decrease population fitness. These evolutionary consequences of FD selection are relevant to modern concerns about population persistence and the capacity of evolution to alleviate extinction risks. But exactly when should we expect FD selection to increase versus decrease absolute fitness and population growth? And how much of an impact is FD selection expected to have on population persistence versus extinction in changing environments? The answers to these questions have implications for evolutionary rescue under climate change and may inform strategies for managing threatened populations. Here, we revisit the core theory of FD selection, reviewing classical single-locus models of population genetic change and outlining short- and long-run consequences of FD selection for the evolution of population fitness. We then develop a quantitative genetic model of evolutionary rescue in a deteriorating environment, with population persistence hinging upon the evolution of a quantitative trait subject to both frequency-dependent and frequency-independent natural selection. We discuss the empirical literature pertinent to this theory, which supports key assumptions of our model. We show that FD selection can promote population persistence when it aligns with the direction of frequency-independent selection imposed by abiotic environmental conditions. However, under most scenarios of environmental change, FD selection limits a population's evolutionary responsiveness to changing conditions and narrows the rate of environmental change that is evolutionarily tolerable.

Surfing on the seascape: Adaptation in a changing environment

The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation-limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an "adaptive-walk" approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.

Cross-sex genetic correlations for fitness and fitness components: Connecting theoretical predictions to empirical patterns

Sex differences in morphology, physiology, development, and behavior are widespread, yet the sexes inherit nearly identical genomes, causing most traits to exhibit strong and positive cross‐sex genetic correlations. In contrast to most other traits, estimates of cross‐sex genetic correlations for fitness and fitness components (rW fm ) are generally low and occasionally negative, implying that a substantial fraction of standing genetic variation for fitness might be sexually antagonistic (i.e., alleles benefitting one sex harm the other). Nevertheless, while low values of rW fm are often regarded as consequences of sexually antagonistic selection, it remains unclear exactly how selection and variation in quantitative traits interact to determine the sign and magnitude of rW fm , making it difficult to relate empirical estimates of cross‐sex genetic correlations to the evolutionary processes that might shape them. We present simple univariate and multivariate quantitative genetic models that explicitly link patterns of sex‐specific selection and trait genetic variation to the cross‐sex genetic correlation for fitness. We show that rW fm provides an unreliable signal of sexually antagonistic selection for two reasons. First, rW fm is constrained to be less than the cross‐sex genetic correlation for traits affecting fitness, regardless of the nature of selection on the traits. Second, sexually antagonistic selection is an insufficient condition for generating negative cross‐sex genetic correlations for fitness. Instead, negative fitness correlations between the sexes (rW fm <0) can only emerge when selection is sexually antagonistic and the strength of directional selection on each sex is strong relative to the amount of shared additive genetic variation in female and male traits. These results imply that empirical tests of sexual antagonism that are based on estimates of rW fm will be conservative and underestimate its true scope. In light of these theoretical results, we revisit current data on rW fm and sex‐specific selection and find that they are consistent with the theory.

Clownfishes evolution below and above the species level

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.

Quantifying how constraints limit the diversity of viable routes to adaptation

Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

How many ways can evolution solve the same adaptive problem? While convergent adaptation is evident in many organisms at the phenotypic level, we are only beginning to understand how commonly this convergence extends to the genome scale. Quantifying the repeatability of adaptation at the genome scale is therefore critical for assessing how constraints affect the diversity of viable genetic responses. Here, we develop probability-based indices to quantify the deviation between observed repeatability and expectations under a range of null hypotheses, and an estimator of the proportion of loci in the genome that can contribute to adaptation. We demonstrate the usage of these indices with individual-based simulations and example datasets from yeast and conifers and discuss how they differ from previously developed approaches to studying repeatability. Because these indices are unitless, they provide a general approach to quantifying and comparing how constraints drive convergence at the genome scale across a wide range of traits and taxa.

Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

Environmental variability is on the rise in different parts of the earth, and the survival of many species depends on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor such as temperature or pH. How would unpredictability affect adaptation when the environment fluctuates between qualitatively very different kinds of stresses? To answer this question, we subjected laboratory populations of Escherichia coli to selection over ~ 260 generations. The populations faced predictable and unpredictable environmental fluctuations across qualitatively different selection environments, namely, salt and acidic pH. We show that predictability of environmental fluctuations does not play a role in determining the extent of adaptation, although the extent of ancestral adaptation to the chosen selection environments is of key importance.

Phenotypic lag and population extinction in the moving-optimum model: insights from a small-jumps limit

Continuous environmental change-such as slowly rising temperatures-may create permanent maladaptation of natural populations: Even if a population adapts evolutionarily, its mean phenotype will usually lag behind the phenotype favored in the current environment, and if the resulting phenotypic lag becomes too large, the population risks extinction. We analyze this scenario using a moving-optimum model, in which one or more quantitative traits are under stabilizing selection towards an optimal value that increases at a constant rate. We have recently shown that, in the limit of infinitely small mutations and high mutation rate, the evolution of the phenotypic lag converges to an Ornstein-Uhlenbeck process around a long-term equilibrium value. Both the mean and the variance of this equilibrium lag have simple analytical formulas. Here, we study the properties of this limit and compare it to simulations of an evolving population with finite mutational effects. We find that the "small-jumps limit" provides a reasonable approximation, provided the mean lag is so large that the optimum cannot be reached by a single mutation. This is the case for fast environmental change and/or weak selection. Our analysis also provides insights into population extinction: Even if the mean lag is small enough to allow a positive growth rate, stochastic fluctuations of the lag will eventually cause extinction. We show that the time until this event follows an exponential distribution, whose mean depends strongly on a composite parameter that relates the speed of environmental change to the adaptive potential of the population.

Genetic adaptation as a biological buffer against climate change: Potential and limitations

Climate change profoundly impacts ecosystems and their biota, resulting in range shifts, novel interactions, food web alterations, changed intensities of host-parasite interactions, and extinctions. An increasing number of studies have documented evolutionary changes in traits such as phenology and thermal tolerance. In this opinion paper, we argue that, while evolutionary responses have the potential to provide a buffer against extinctions or range shifts, a number of constraints and complexities blur this simple prediction. First, there are limits to evolutionary potential both in terms of genetic variation and demographic effects, and these limits differ strongly among taxa and populations. Second, there can be costs associated with genetic adaptation, such as a reduced evolutionary potential towards other (human-induced) environmental stressors or direct fitness costs due to tradeoffs. Third, the differential capacity of taxa to genetically respond to climate change results in novel interactions because different organism groups respond to a different degree with local compared to regional (dispersal and range shift) responses. These complexities result in additional changes in the selection pressures on populations. We conclude that evolution can provide an initial buffer against climate change for some taxa and populations but does not guarantee their survival. It does not necessarily result in reduced extinction risks across the range of taxa in a region or continent. Yet, considering evolution is crucial, as it is likely to strongly change how biota will respond to climate change and will impact which taxa will be the winners or losers at the local, metacommunity and regional scales.

Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness

Antagonistic pleiotropy (AP)-where alleles of a gene increase some components of fitness at a cost to others-can generate balancing selection, and contribute to the maintenance of genetic variation in fitness traits, such as survival, fecundity, fertility, and mate competition. Previous theory suggests that AP is unlikely to maintain variation unless antagonistic selection is strong, or AP alleles exhibit pronounced differences in genetic dominance between the affected traits. We show that conditions for balancing selection under AP expand under the likely scenario that the strength of selection on each fitness component differs between the sexes. Our model also predicts that the vast majority of balanced polymorphisms have sexually antagonistic effects on total fitness, despite the absence of sexual antagonism for individual fitness components. We conclude that AP polymorphisms are less difficult to maintain than predicted by prior theory, even under our conservative assumption that selection on components of fitness is universally sexually concordant. We discuss implications for the maintenance of genetic variation, and for inferences of sexual antagonism that are based on sex-specific phenotypic selection estimates-many of which are based on single fitness components.

Both life-history plasticity and local adaptation will shape range-wide responses to climate warming in the tundra plant Silene acaulis

Many predictions of how climate change will impact biodiversity have focused on range shifts using species-wide climate tolerances, an approach that ignores the demographic mechanisms that enable species to attain broad geographic distributions. But these mechanisms matter, as responses to climate change could fundamentally differ depending on the contributions of life-history plasticity vs. local adaptation to species-wide climate tolerances. In particular, if local adaptation to climate is strong, populations across a species' range-not only those at the trailing range edge-could decline sharply with global climate change. Indeed, faster rates of climate change in many high latitude regions could combine with local adaptation to generate sharper declines well away from trailing edges. Combining 15 years of demographic data from field populations across North America with growth chamber warming experiments, we show that growth and survival in a widespread tundra plant show compensatory responses to warming throughout the species' latitudinal range, buffering overall performance across a range of temperatures. However, populations also differ in their temperature responses, consistent with adaptation to local climate, especially growing season temperature. In particular, warming begins to negatively impact plant growth at cooler temperatures for plants from colder, northern populations than for those from warmer, southern populations, both in the field and in growth chambers. Furthermore, the individuals and maternal families with the fastest growth also have the lowest water use efficiency at all temperatures, suggesting that a trade-off between growth and water use efficiency could further constrain responses to forecasted warming and drying. Taken together, these results suggest that populations throughout species' ranges could be at risk of decline with continued climate change, and that the focus on trailing edge populations risks overlooking the largest potential impacts of climate change on species' abundance and distribution.

Genetic constraints on adaptation: a theoretical primer for the genomics era

Genetic constraints are features of inheritance systems that slow or prohibit adaptation. Several population genetic mechanisms of constraint have received sustained attention within the field since they were first articulated in the early 20th century. This attention is now reflected in a rich, and still growing, theoretical literature on the genetic limits to adaptive change. In turn, empirical research on constraints has seen a rapid expansion over the last two decades in response to changing interests of evolutionary biologists, along with new technologies, expanding data sets, and creative analytical approaches that blend mathematical modeling with genomics. Indeed, one of the most notable and exciting features of recent progress in genetic constraints is the close connection between theoretical and empirical research. In this review, we discuss five major population genetic contexts of genetic constraint: genetic dominance, pleiotropy, fitness trade-offs between types of individuals of a population, sign epistasis, and genetic linkage between loci. For each, we outline historical antecedents of the theory, specific contexts where constraints manifest, and their quantitative consequences for adaptation. From each of these theoretical foundations, we discuss recent empirical approaches for identifying and characterizing genetic constraints, each grounded and motivated by this theory, and outline promising areas for future work.

Adaptations of an RNA virus to increasing thermal stress

Environments can change in incremental fashions, where a shift from one state to another occurs over multiple organismal generations. The rate of the environmental change is expected to influence how and how well populations adapt to the final environmental state. We used a model system, the lytic RNA bacteriophage Φ6, to investigate this question empirically. We evolved viruses for thermostability by exposing them to heat shocks that increased to a maximum temperature at different rates. We observed increases in the ability of many heat-shocked populations to survive high temperature heat shocks. On their first exposure to the highest temperature, populations that experienced a gradual increase in temperature had higher average survival than populations that experienced a rapid temperature increase. However, at the end of the experiment, neither the survival of populations at the highest temperature nor the number of mutations per population varied significantly according to the rate of thermal change. We also evaluated mutations from the endpoint populations for their effects on viral thermostability and growth. As expected, some mutations did increase viral thermostability. However, other mutations decreased thermostability but increased growth rate, suggesting that benefits of an increased replication rate may have sometimes outweighed the benefits of enhanced thermostability. Our study highlights the importance of considering the effects of multiple selective pressures, even in environments where a single factor changes.

Stochastic Evolutionary Demography under a Fluctuating Optimum Phenotype

Many natural populations exhibit temporal fluctuations in abundance that are consistent with external forcing by a randomly changing environment. As fitness emerges from an interaction between the phenotype and the environment, such demographic fluctuations probably include a substantial contribution from fluctuating phenotypic selection. We study the stochastic population dynamics of a population exposed to random (plus possibly directional) changes in the optimum phenotype for a quantitative trait that evolves in response to this moving optimum. We derive simple analytical predictions for the distribution of log population size over time both transiently and at stationarity under Gompertz density regulation. These predictions are well matched by population- and individual-based simulations. The log population size is approximately reverse gamma distributed, with a negative skew causing an excess of low relative to high population sizes, thus increasing extinction risk relative to a symmetric (e.g., normal) distribution with the same mean and variance. Our analysis reveals how the mean and variance of log population size change with the variance and autocorrelation of deviations of the evolving mean phenotype from the optimum. We apply our results to the analysis of evolutionary rescue in a stochastic environment and show that random fluctuations in the optimum can substantially increase extinction risk by both reducing the expected growth rate and increasing the variance of population size by several orders of magnitude.